Definitive prenatal diagnosis of fetal aneuploidy is currently performed using chorionic villus sampling (CVS) or amniocentesis. These are invasive, expensive and somewhat risky approaches that must be performed by experienced clinicians and are generally only offered to expectant mothers considered to be at elevated risk of carrying a genetically abnormal fetus. Low cost minimally invasive screening is routinely used across the maternal age range but this is based upon the quantification of serum proteins that are surrogate markers of the underlying genetic abnormality and do not achieve desirable levels of sensitivity and specificity (Wapner et al., N. Eng J. Med. 349: 1405-13, 2003; Alfirevic and Neilson, BMJ 326: 811-2, 2004; Malone et al., N Engl. J. Med 353: 2001-11, 2005).
An attractive alternative involves the analysis of placentally-derived nucleic acids in maternal plasma to characterize specific features of the fetal genome (Lo, Ann. NY. Acad. Sci. 1137: 140-3, 2008). However, because of the technical challenge of distinguishing maternally inherited fetal alleles from endogenous maternal DNA this approach has largely been limited to the detection of paternally inherited disease-causing mutations (Zimmermann et al., Methods Mol Med 132: 43-49, 2007; Li et al., Prenat Diag 27: 11-7, 2007). Differential DNA methylation patterns between the placental and maternal leukocyte genomes at distinct loci have been used to determine the fetal genotype (Lo et al., PNAS 104: 13116-21, 2007; Lo et al., Nat Med 13:218-23, 2007). Specific polymerase chain reaction (PCR)-based assays were used that amplify a given methylated (placental), but not an unmethylated (maternal) locus (or visa versa) in DNA obtained from maternal plasma (Tsui et al., Prenat Diag 27: 1212-8, 2007; Tong et al., Clin Chem 53: 1906-14, 2007; Chan et al., Clin Chem 52: 2211-8, 2006; Tong et al., Clin Chem 52: 2194-202, 2006). However, a need remains for sensitive and specific non-invasive methods that can be used to diagnose fetal conditions, such as aneuploidy, using the placental methylome.